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Critical assessment of missense variant effect predictors on disease-relevant variant data Rastogi, Ruchir; Chung, Ryan; Li, Sindy; Li, Chang; Lee, Kyoungyeul; Woo, Junwoo; Kim, Dong-Wook; Keum, Changwon; Babbi, Giulia; Martelli, Pier Luigi; Savojardo, Castrense; Casadio, Rita; Chennen, Kirsley; Weber, Thomas; Poch, Olivier; Ancien, Francois; Cia, Gabriel; Pucci, Fabrizio; Raimondi, Daniele; Vranken, Wim; Rooman, Marianne; Marquet, Celine; Olenyi, Tobias; Rost, Burkhard; Andreoletti, Gaia; Kamandula, Akash; Peng, Yisu; Bakolitsa, Constantina; Mort, Matthew; Cooper, David N.; Bergquist, Timothy; Pejaver, Vikas; Liu, Xiaoming; Radivojac, Predrag; Brenner, Steven E.; Ioannidis, Nilah M. Share Save
A differentiated β-globin gene replacement strategy uses heterologous introns to restore physiological expression Wallace, Kirby A.; Gerstenberg, Trevor L.; Ennis, Craig L.; Perez-Bermejo, Juan A.; Partridge, James R.; Bandoro, Christopher; Matern, William M.; Andreoletti, Gaia; Krassovsky, Kristina; Kabir, Shaheen; Lalisan, Cassandra D.; Churi, Aishwarya R.; Chew, Glen M.; Corbo, Lana; Vincelette, Jon E.; Klasson, Timothy D.; Silva, Brian J.; Strukov, Yuri G.; Quejarro, B. Joy; Hill, Kaisle A.; Treusch, Sebastian; Grogan, Jane L.; Dever, Daniel P.; Porteus, Matthew H.; Wienert, Beeke Share Save
Functional screening in human HSPCs identifies optimized protein-based enhancers of Homology Directed Repair Perez-Bermejo, Juan A.; Efagene, Oghene; Matern, William M.; Holden, Jeffrey K.; Kabir, Shaheen; Chew, Glen M.; Andreoletti, Gaia; Catton, Eniola; Ennis, Craig L.; Garcia, Angelica; Gerstenberg, Trevor L.; Hill, Kaisle A.; Jain, Aayami; Krassovsky, Kristina; Lalisan, Cassandra D.; Lord, Daniel; Quejarro, B. Joy; Sales-Lee, Jade; Shah, Meet; Silva, Brian J.; Skowronski, Jason; Strukov, Yuri G.; Thomas, Joshua; Veraz, Michael; Vijay, Twaritha; Wallace, Kirby A.; Yuan, Yue; Grogan, Jane L.; Wienert, Beeke; Lahiri, Premanjali; Treusch, Sebastian; Dever, Daniel P.; Soros, Vanessa B.; Partridge, James R.; Seim, Kristen L. Share Save
CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods Jain, Shantanu; Bakolitsa, Constantina; Brenner, Steven E.; Radivojac, Predrag; Moult, John; Repo, Susanna; Hoskins, Roger A.; Andreoletti, Gaia; Barsky, Daniel; Chellapan, Ajithavalli; Chu, Hoyin; Dabbiru, Navya; Kollipara, Naveen K.; Ly, Melissa; Neumann, Andrew J.; Pal, Lipika R.; Odell, Eric; Pandey, Gaurav; Peters-Petrulewicz, Robin C.; Srinivasan, Rajgopal; Yee, Stephen F.; Yeleswarapu, Sri Jyothsna; Zuhl, Maya; Adebali, Ogun; Patra, Ayoti; Beer, Michael A.; Hosur, Raghavendra; Peng, Jian; Bernard, Brady M.; Berry, Michael; Dong, Shengcheng; Boyle, Alan P.; Adhikari, Aashish; Chen, Jingqi; Hu, Zhiqiang; Wang, Robert; Wang, Yaqiong; Miller, Maximilian; Wang, Yanran; Bromberg, Yana; Turina, Paola; Capriotti, Emidio; Han, James J.; Ozturk, Kivilcim; Carter, Hannah; Babbi, Giulia; Bovo, Samuele; Di Lena, Pietro; Martelli, Pier Luigi; Savojardo, Castrense; Casadio, Rita; Cline, Melissa S.; De Baets, Greet; Bonache, Sandra; Diez, Orland; Gutierrez-Enriquez, Sara; Fernandez, Alejandro; Montalban, Gemma; Ootes, Lars; Ozkan, Selen; Padilla, Natalia; Riera, Casandra; De la Cruz, Xavier; Diekhans, Mark; Huwe, Peter J.; Wei, Qiong; Xu, Qifang; Dunbrack, Roland L.; Gotea, Valer; Elnitski, Laura; Margolin, Gennady; Fariselli, Piero; Kulakovskiy, Ivan V.; Makeev, Vsevolod J.; Penzar, Dmitry D.; Vorontsov, Ilya E.; Favorov, Alexander V.; Forman, Julia R.; Hasenahuer, Marcia; Fornasari, Maria S.; Parisi, Gustavo; Avsec, Ziga; Celik, Muhammed H.; Thi Yen Duong Nguyen; Gagneur, Julien; Shi, Fang-Yuan; Edwards, Matthew D.; Guo, Yuchun; Tian, Kevin; Zeng, Haoyang; Gifford, David K.; Goke, Jonathan; Zaucha, Jan; Gough, Julian; Ritchie, Graham R. S.; Frankish, Adam; Mudge, Jonathan M.; Harrow, Jennifer; Young, Erin L.; Yu, Yao; Huff, Chad D.; Murakami, Katsuhiko; Nagai, Yoko; Imanishi, Tadashi; Mungall, Christopher J.; Jacobsen, Julius O. B.; Kim, Dongsup; Jeong, Chan-Seok; Jones, David T.; Li, Mulin Jun; Guthrie, Violeta Beleva; Bhattacharya, Rohit; Chen, Yun-Ching; Douville, Christopher; Fan, Jean; Kim, Dewey; Masica, David; Niknafs, Noushin; Sengupta, Sohini; Tokheim, Collin; Turner, Tychele N.; Yeo, Hui Ting Grace; Karchin, Rachel; Shin, Sunyoung; Welch, Rene; Keles, Sunduz; Li, Yue; Kellis, Manolis; Corbi-Verge, Carles; Strokach, Alexey V.; Kim, Philip M.; Klein, Teri E.; Mohan, Rahul; Sinnott-Armstrong, Nicholas A.; Wainberg, Michael; Kundaje, Anshul; Gonzaludo, Nina; Mak, Angel C. Y.; Chhibber, Aparna; Lam, Hugo Y. K.; Dahary, Dvir; Fishilevich, Simon; Lancet, Doron; Lee, Insuk; Bachman, Benjamin; Katsonis, Panagiotis; Lua, Rhonald C.; Wilson, Stephen J.; Lichtarge, Olivier; Bhat, Rajendra R.; Sundaram, Laksshman; Viswanath, Vivek; Bellazzi, Riccardo; Nicora, Giovanna; Rizzo, Ettore; Limongelli, Ivan; Mezlini, Aziz M.; Chang, Ray; Kim, Serra; Lai, Carmen; O'Connor, Robert; Topper, Scott; van den Akker, Jeroen; Zhou, Alicia Y.; Zimmer, Anjali D.; Mishne, Gilad; Bergquist, Timothy R.; Breese, Marcus R.; Guerrero, Rafael F.; Jiang, Yuxiang; Kiga, Nikki; Li, Biao; Mort, Matthew; Pagel, Kymberleigh A.; Pejaver, Vikas; Stamboulian, Moses H.; Thusberg, Janita; Mooney, Sean D.; Teerakulkittipong, Nuttinee; Cao, Chen; Kundu, Kunal; Yin, Yizhou; Yu, Chen-Hsin; Kleyman, Michael; Lin, Chiao-Feng; Stackpole, Mary; Mount, Stephen M.; Eraslan, Gokcen; Mueller, Nikola S.; Naito, Tatsuhiko; Rao, Aliz R.; Azaria, Johnathan R.; Brodie, Aharon; Ofran, Yanay; Garg, Aditi; Pal, Debnath; Hawkins-Hooker, Alex; Kenlay, Henry; Reid, John; Mucaki, Eliseos J.; Rogan, Peter K.; Schwarz, Jana M.; Searls, David B.; Lee, Gyu Rie; Seok, Chaok; Kramer, Andreas; Shah, Sohela; Huang, ChengLai V.; Kirsch, Jack F.; Shatsky, Maxim; Cao, Yue; Chen, Haoran; Karimi, Mostafa; Moronfoye, Oluwaseyi; Sun, Yuanfei; Shen, Yang; Shigeta, Ron; Ford, Colby T.; Nodzak, Conor; Uppal, Aneeta; Shi, Xinghua; Joseph, Thomas; Kotte, Sujatha; Rana, Sadhna; Rao, Aditya; Saipradeep, V. G.; Sivadasan, Naveen; Sunderam, Uma; Stanke, Mario; Su, Andrew; Adzhubey, Ivan; Jordan, Daniel M.; Sunyaev, Shamil; Rousseau, Frederic; Schymkowitz, Joost; Van Durme, Joost; Tavtigian, Sean V.; Carraro, Marco; Giollo, Manuel; Tosatto, Silvio C. E.; Adato, Orit; Carmel, Liran; Cohen, Noa E.; Fenesh, Izila; Holtzer, Iamar; Juven-Gershon, Tamar; Unger, Ron; Niroula, Abhishek; Olatubosun, Ayodeji; Valiaho, Jouni; Yang, Yang; Vihinen, Mauno; Wahl, Mary E.; Chang, Billy; Chong, Ka Chun; Hu, Inchi; Sun, Rui; Wu, William Ka Kei; Xia, Xiaoxuan; Zee, Benny C.; Wang, Maggie H.; Wang, Meng; Wu, Chunlei; Lu, Yutong; Chen, Ken; Yang, Yuedong; Yates, Christopher M.; Kreimer, Anat; Yan, Zhongxia; Yosef, Nir; Zhao, Huying; Wei, Zhipeng; Yao, Zhaomin; Zhou, Fengfeng; Folkman, Lukas; Zhou, Yaoqi; Daneshjou, Roxana; Altman, Russ B.; Inoue, Fumitaka; Ahituv, Nadav; Arkin, Adam P.; Lovisa, Federica; Bonvini, Paolo; Bowdin, Sarah; Gianni, Stefano; Mantuano, Elide; Minicozzi, Velia; Novak, Leonore; Pasquo, Alessandra; Pastore, Annalisa; Petrosino, Maria; Puglisi, Rita; Toto, Angelo; Veneziano, Liana; Chiaraluce, Roberta; Ball, Mad P.; Bobe, Jason R.; Church, George M.; Consalvi, Valerio; Mort, Matthew; Cooper, David N.; Buckley, Bethany A.; Sheridan, Molly B.; Cutting, Garry R.; Scaini, Maria Chiara; Cygan, Kamil J.; Fredericks, Alger M.; Glidden, David T.; Neil, Christopher; Rhine, Christy L.; Fairbrother, William G.; Alontaga, Aileen Y.; Fenton, Aron W.; Matreyek, Kenneth A.; Starita, Lea M.; Fowler, Douglas M.; Loescher, Britt-Sabina; Franke, Andre; Adamson, Scott I.; Graveley, Brenton R.; Gray, Joe W.; Malloy, Mary J.; Kane, John P.; Kousi, Maria; Katsanis, Nicholas; Schubach, Max; Kircher, Martin; Tang, Paul L. F.; Kwok, Pui-Yan; Lathrop, Richard H.; Clark, Wyatt T.; Yu, Guoying K.; LeBowitz, Jonathan H.; Benedicenti, Francesco; Bettella, Elisa; Bigoni, Stefania; Cesca, Federica; Mammi, Isabella; Marino-Bus-Ije, Cristina; Milani, Donatella; Peron, Angela; Polli, Roberta; Sartori, Stefano; Stanzial, Franco; Ioldo, Irene; Turolla, Licia; Aspromonte, Maria C.; Bellini, Mariagrazia; Leonardi, Emanuela; Liu, Xiaoming; Marshall, Christian; McCombie, W. Richard; Elefanti, Lisa; Menin, Chiara; Meyn, M. Stephen; Murgia, Alessandra; Nadeau, Kari C. Y.; Neuhausen, Susan L.; Nussbaum, Robert L.; Pirooznia, Mehdi; Potash, James B.; Dimster-Denk, Dago F.; Rine, Jasper D.; Sanford, Jeremy R.; Snyder, Michael; Tavtigian, Sean V.; Cole, Alina G.; Sun, Song; Verby, Marta W.; Weile, Jochen; Roth, Frederick P.; Tewhey, Ryan; Sabeti, Pardis C.; Campagna, Joan; Refaat, Marwan M.; Wojciak, Julianne; Grubb, Soren; Schmitt, Nicole; Shendure, Jay; Spurdle, Amanda B.; Stavropoulos, Dimitri J.; Walton, Nephi A.; Zandi, Peter P.; Ziv, Elad; Burke, Wylie; Chen, Flavia; Carr, Lawrence R.; Martinez, Selena; Paik, Jodi; Harris-Wai, Julie; Yarborough, Mark; Fullerton, Stephanie M.; Koenig, Barbara A.; McInnes, Gregory; Shigaki, Dustin; Chandonia, John-Marc; Furutsuki, Mabel; Kasak, Laura; Yu, Changhua; Chen, Rui; Cline, Melissa S.; Pandey, Gaurav; Friedberg, Iddo; Getz, Gad A.; Cong, Qian; Kinch, Lisa N.; Zhang, Jing; Grishin, Nick V.; Voskanian, Alin; Kann, Maricel G.; Clark, Wyatt T.; Tran, Elizabeth; Ioannidis, Nilah M.; Hunter, Jesse M.; Udani, Rupa; Cai, Binghuang; Morgan, Alexander A.; Sokolov, Artem; Stuart, Joshua M.; Tavtigian, Sean V.; Minervini, Giovanni; Monzon, Alexander M.; Batzoglou, Serafim; Butte, Atul J.; Church, George M.; Greenblatt, Marc S.; Hart, Reece K.; Hernandez, Ryan; Hubbard, Tim J. P.; Kahn, Scott; O'Donnell-Luria, Anne; Ng, Pauline C.; Shon, John; Tavtigian, Sean V.; Veltman, Joris; Zook, Justin M. Share Save
High-throughput transcriptome analyses from ASPIRO, a phase 1/2/3 study of gene replacement therapy for X-linked myotubular myopathy Andreoletti, Gaia; Romano, Oriana; Chou, Hsin-Jung; Sefid-Dashti, Mahjoubeh J.; Grilli, Andrea; Chen, Clarice; Lakshman, Neema; Purushothaman, Pravin; Varfaj, Fatbardha; Mavilio, Fulvio; Bicciato, Silvio; Urbinati, Fabrizia Share Save
Loss of Mtm1 causes cholestatic liver disease in a model of X-linked myotubular myopathy Karolczak, Sophie; Deshwar, Ashish R.; Aristegui, Evangelina; Kamath, Binita M.; Lawlor, Michael W.; Andreoletti, Gaia; Volpatti, Jonathan; Ellis, Jillian L.; Yin, Chunyue; Dowling, James J. Share Save
Transcriptomics-based drug repositioning pipeline identifies therapeutic candidates for COVID-19 Le, Brian L.; Andreoletti, Gaia; Oskotsky, Tomiko; Vallejo-Gracia, Albert; Rosales, Romel; Yu, Katharine; Kosti, Idit; Leon, Kristoffer E.; Bunis, Daniel G.; Li, Christine; Kumar, G. Renuka; White, Kris M.; Garcia-Sastre, Adolfo; Ott, Melanie; Sirota, Marina Share Save
Crowdsourcing assessment of maternal blood multi-omics for predicting gestational age and preterm birth Tarca, Adi L.; Pataki, Balint Armin; Romero, Roberto; Sirota, Marina; Guan, Yuanfang; Kutum, Rintu; Gomez-Lopez, Nardhy; Done, Bogdan; Bhatti, Gaurav; Yu, Thomas; Andreoletti, Gaia; Chaiworapongsa, Tinnakorn; Hassan, Sonia S.; Hsu, Chaur-Dong; Aghaeepour, Nima; Stolovitzky, Gustavo; Csabai, Istvan; Costello, James C. Share Save
Transcriptomic analysis of immune cells in a multi-ethnic cohort of systemic lupus erythematosus patients identifies ethnicity- and disease-specific expression signatures Andreoletti, Gaia; Lanata, Cristina M.; Trupin, Laura; Paranjpe, Ishan; Jain, Tia S.; Nititham, Joanne; Taylor, Kimberly E.; Combes, Alexis J.; Maliskova, Lenka; Ye, Chun Jimmie; Katz, Patricia; Dall'Era, Maria; Yazdany, Jinoos; Criswell, Lindsey A.; Sirota, Marina Share Save
BRD4 (Bromodomain-Containing Protein 4) Interacts with GATA4 (GATA Binding Protein 4) to Govern Mitochondrial Homeostasis in Adult Cardiomyocytes Padmanabhan, Arun; Alexanian, Michael; Linares-Saldana, Ricardo; Gonzalez-Teran, Barbara; Andreoletti, Gaia; Huang, Yu; Connolly, Andrew J.; Kim, Wonho; Hsu, Austin; Duan, Qiming; Winchester, Sarah A. B.; Felix, Franco; Perez-Bermejo, Juan A.; Wang, Qiaohong; Li, Li; Shah, Parisha P.; Haldar, Saptarsi M.; Jain, Rajan; Srivastava, Deepak Share Save
Conserved Epigenetic Regulatory Logic Infers Genes Governing Cell Identity Shim, Woo Jun; Sinniah, Enakshi; Xu, Jun; Vitrinel, Burcu; Alexanian, Michael; Andreoletti, Gaia; Shen, Sophie; Sun, Yuliangzi; Balderson, Brad; Boix, Carles; Peng, Guangdun; Jing, Naihe; Wang, Yuliang; Kellis, Manolis; Tam, Patrick P. L.; Smith, Aaron; Piper, Michael; Christiaen, Lionel; Quan Nguyen; Boden, Mikael; Palpant, Nathan J. Share Save
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Assessment of patient clinical descriptions and pathogenic variants from gene panel sequences in the CAGI-5 intellectual disability challenge Carraro, Marco; Monzon, Alexander Miguel; Chiricosta, Luigi; Reggiani, Francesco; Aspromonte, Maria Cristina; Bellini, Mariagrazia; Pagel, Kymberleigh; Jiang, Yuxiang; Radivojac, Predrag; Kundu, Kunal; Pal, Lipika R.; Yin, Yizhou; Limongelli, Ivan; Andreoletti, Gaia; Moult, John; Wilson, Stephen J.; Katsonis, Panagiotis; Lichtarge, Olivier; Chen, Jingqi; Wang, Yaqiong; Hu, Zhiqiang; Brenner, Steven E.; Ferrari, Carlo; Murgia, Alessandra; Tosatto, Silvio C. E.; Leonardi, Emanuela Share Save
Performance of computational methods for the evaluation of pericentriolar material 1 missense variants in CAGI-5 Monzon, Alexander Miguel; Carraro, Marco; Chiricosta, Luigi; Reggiani, Francesco; Han, James; Ozturk, Kivilcim; Wang, Yanran; Miller, Maximilian; Bromberg, Yana; Capriotti, Emidio; Savojardo, Castrense; Babbi, Giulia; Martelli, Pier L.; Casadio, Rita; Katsonis, Panagiotis; Lichtarge, Olivier; Carter, Hannah; Kousi, Maria; Katsanis, Nicholas; Andreoletti, Gaia; Moult, John; Brenner, Steven E.; Ferrari, Carlo; Leonardi, Emanuela; Tosatto, Silvio C. E. Share Save
Assessment of predicted enzymatic activity of α-N-acetylglucosaminidase variants of unknown significance for CAGI 2016 Clark, Wyatt T.; Kasak, Laura; Bakolitsa, Constantina; Hu, Zhiqiang; Andreoletti, Gaia; Babbi, Giulia; Bromberg, Yana; Casadio, Rita; Dunbrack, Roland; Folkman, Lukas; Ford, Colby T.; Jones, David; Katsonis, Panagiotis; Kundu, Kunal; Lichtarge, Olivier; Martelli, Pier L.; Mooney, Sean D.; Nodzak, Conor; Pal, Lipika R.; Ivojac, Pred Rag Rad; Savojardo, Castrense; Shi, Xinghua; Zhou, Yaoqi; Uppal, Aneeta; Xu, Qifang; Yin, Yizhou; Pejaver, Vikas; Wang, Meng; Wei, Liping; Moult, John; Yu, Guoying Karen; Brenner, Steven E.; LeBowitz, Jonathan H. Share Save
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Assessing the performance of in silico methods for predicting the pathogenicity of variants in the gene CHEK2, among Hispanic females with breast cancer Voskanian, Alin; Katsonis, Panagiotis; Lichtarge, Olivier; Pejaver, Vikas; Radivojac, Predrag; Mooney, Sean D.; Capriotti, Emidio; Bromberg, Yana; Wang, Yanran; Miller, Max; Martelli, Pier Luigi; Savojardo, Castrense; Babbi, Giulia; Casadio, Rita; Cao, Yue; Sun, Yuanfei; Shen, Yang; Garg, Aditi; Pal, Debnath; Yu, Yao; Huff, Chad D.; Tavtigian, Sean, V; Young, Erin; Neuhausen, Susan L.; Ziv, Elad; Pal, Lipika R.; Andreoletti, Gaia; Brenner, Steven E.; Kann, Maricel G. Share Save
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